schema-version-bump.yml

name: Schema Version Bump Workflow

on:
  workflow_dispatch:
    inputs:
      is-major-schema-bump:
        description: "Set to 'true' to kickoff major schema update; otherwise trigger a minor schema update"
        required: true
        default: 'false'

permissions:
  id-token: write
  contents: write
  pull-requests: write

jobs:
  ontology-dry-run:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"
      - name: Python cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install dependencies
        run: |
          pip install -r scripts/schema_bump_dry_run_ontologies/requirements.txt
      - name: Configure AWS Credentials
        uses: aws-actions/configure-aws-credentials@v4
        with:
          aws-region: us-west-2
          role-to-assume: ${{ secrets.AWS_PROD_ROLE_TO_ASSUME }}
          role-duration-seconds: 2700
      - name: Pull AWS Secrets
        uses: aws-actions/aws-secretsmanager-get-secrets@v2
        with:
          secret-ids:
            AUTH0_SECRETS, corpora/backend/prod/auth0-secret
      - name: Run Dry-Run Script
        run: python3 -m scripts.schema_bump_dry_run_ontologies.ontology_bump_dry_run
        env:
          corpus_env: "prod"
      - name: Store JSON with Replaced By Ontology Term Mappings
        uses: actions/cache/save@v4
        with:
          path: "./replaced-by.json"
          key: replaced-by-map
      - name: upload dry run to slack
        run: |
          curl -F file=@ontologies-curator-report.txt -F "initial_comment=Ontology Dry Run Report" -F channels=${{secrets.SLACK_CURATOR_REPORTING_CHANNEL}} -H "Authorization: Bearer ${{secrets.SLACK_CURATOR_REPORTING_APP_AUTH}}" https://slack.com/api/files.upload

  gencode-dry-run:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"
      - name: Python cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install dependencies
        run: |
          pip install -r scripts/schema_bump_dry_run_genes/requirements.txt
      - name: Configure AWS Credentials
        uses: aws-actions/configure-aws-credentials@v4
        with:
          aws-region: us-west-2
          role-to-assume: ${{ secrets.AWS_PROD_ROLE_TO_ASSUME }}
          role-duration-seconds: 2700
      - name: Pull AWS Secrets
        uses: aws-actions/aws-secretsmanager-get-secrets@v2
        with:
          secret-ids:
            AUTH0_SECRETS, corpora/backend/prod/auth0-secret
      - name: Check if any GENCODE csv files have changed
        id: changed-files
        uses: tj-actions/changed-files@v44
        with:
          files: cellxgene_schema_cli/cellxgene_schema/gencode_files/*.csv.gz
      - name: Run Dry-Run Script
        if: steps.changed-files.outputs.any_changed == 'true'
        run: python3 -m scripts.schema_bump_dry_run_genes.gene_bump_dry_run
        env:
          corpus_env: "prod"
      - name: upload to slack
        if: steps.changed-files.outputs.any_changed == 'true'
        run: |
          curl -F file=@genes-curator-report.txt -F "initial_comment=Gene Dry Run Report" -F channels=${{secrets
          .SLACK_CURATOR_REPORTING_CHANNEL}} -H "Authorization: Bearer ${{secrets.SLACK_CURATOR_REPORTING_APP_AUTH}}" https://slack.com/api/files.upload

  generate-conversion-script:
    runs-on: ubuntu-latest
    needs: ontology-dry-run
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.ref }} # checking out the last commit to this branch
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.11
      - name: Python cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install dependencies
        run: |
          pip install -r scripts/migration_assistant/requirements.txt
      - name: Retrieve Replaced By Ontology Term Mapping
        uses: actions/cache/restore@v4
        with:
          path: ./replaced-by.json
          key: replaced-by-map
      - name: Run Conversion Script Generator
        run: |
          make generate-conversion-script
      - name: Get Version
        id: get_version
        run: |
          echo "old_version=$(make show-current-version)" >> $GITHUB_ENV
      - name: setup git
        run: |
          git config user.name github-actions
          git config user.email github-actions@github.com
      - name: remove diff files
        run: |
          git rm --ignore-unmatch ./cellxgene_schema_cli/cellxgene_schema/gencode_files/*_diff.txt
      - name: Bump Patch Version
        if: ${{ github.event.inputs.is-major-schema-bump }} == 'false'
        run: |
          pip install bumpversion
          pip install wheel
          bumpversion --config-file .bumpversion.cfg minor --allow-dirty
          bumpversion --config-file .bumpversion.cfg prerel --allow-dirty --tag
          echo "new_version=$(make show-current-version)" >> $GITHUB_ENV
      - name: Bump RC to Major Version
        if: ${{ github.event.inputs.is-major-schema-bump }} == 'true'
        run: |
          pip install bumpversion
          pip install wheel
          bumpversion --config-file .bumpversion.cfg major --allow-dirty
          bumpversion --config-file .bumpversion.cfg prerel --allow-dirty --tag
          echo "new_version=$(make show-current-version)" >> $GITHUB_ENV
      - name: Create Pull Request
        uses: peter-evans/create-pull-request@v6
        with:
          commit-message: 'AUTO: update migrate.py schema_version ${{ env.old_version }}->${{ env.new_version }}'
          title: 'AUTO: update migrate.py schema_version ${{ env.old_version }}->${{ env.new_version }}'
          body: 'This is an automated PR to update migrate.py from schema_version ${{ env.old_version }}->${{ env.new_version }}.'
          branch: auto/update-convert-py-to-${{ env.new_version }}
          base: main
          reviewers: ${{ vars.MIGRATION_REVIEWERS }}
          add-paths: |
            cellxgene_schema_cli/setup.py
            cellxgene_schema_cli/cellxgene_schema/__init__.py
            cellxgene_schema_cli/cellxgene_schema/migrate.py
            .bumpversion.cfg